Solanum lycopersicum Chromosome 4 Sequencing Update SOL Germany– October 2008 Wellcome Trust Medical Photographic Library.

Slides:

Advertisements

Similar presentations

Chr9 A ntonio Granell IBMCP-Valencia Spain Tomato Sequencing, Madison July 2006.

Advertisements

Progress on the sequencing of the euchromatic gene rich space of chromosome 6 of Solanum lycopersicum cv. Heinz 1706 Sander Peters Cologne Oct 2008.

The International Tomato Sequencing Project: The first Cornerstone of the SOL Project Lukas Mueller on behalf of International SOL Tomato Sequencing Project.

US Tomato sequencing project update January 14, 2007.

PAA / Solanaceae July 23-27, Madison, Wisconsin, USA Sequencing the gene-rich space of tomato chromosome 7 Current status of the French effort.

Sequencing Status of the Chromosome 8 and New Marker Development toward a Genetic Map Construction between Micro-Tom and Ailsa Craig SOL Genomics Workshop.

Sequencing Tomato Chr9 Tomato Sequencing Meeting PAG XV 2007 San Diego, 14 January 2007 Antonio Granell IBMCP, Valencia.

Expanding the Tool Kit for BAC Extension Summary of completion criteria developed for NSF Tomato Sequencing Workshop January 14, 2007.

International Tomato Finishing Workshop Wellcome Trust Sanger Institute April 2007 Wellcome Trust Medical Photographic Library.

Novel multi-platform next generation assembly methods for mammalian genomes The Baylor College of Medicine, Australian Government and University of Connecticut.

UK -Tomato Chromosome Four Sarah Butcher Bioinformatics Support Service Centre For Bioinformatics Imperial College London

Use of FISH in sequencing tomato chromosome 6 René Klein Lankhorst Hans de Jong Korea meeting 2007.

Genome sequencing. Vocabulary Bac: Bacterial Artificial Chromosome: cloning vector for yeast Pac, cosmid, fosmid, plasmid: cloning vectors for E. coli.

EU-SOL 2008 November 13-16, Toulouse, FRANCE CHROMOSOME 7 SEQUENCING Current status and perspective TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497.

Presentation on genome sequencing. Genome: the complete set of gene of an organism Genome annotation: the process by which the genes, control sequences.

Plant and Animal Genome Conference January 11, 2009.

Chromosome 8 Sequencing: Current Status and Future Prospects toward Finishing Shusei Sato, Erika Asamizu, Takakazu Kaneko, Hiroyuki Fukuoka, Satoshi Tabata.

Kerstin Howe, Mario Caccamo, Ian Sealy The Zebrafish Genome Sequencing Project Bioinformatics resources.

The New Zealand Institute for Plant & Food Research Limited Potato Genome Sequencing Consortium, notes from the edge Dr Susan Thomson, Dr Mark Fiers, Dr.

Tomato Chromosome 4: A Mapping & Sequencing Update 28 th September 2005 Christine Nicholson Mapping Core Group Welcome Trust Sanger Institute, UK.

Update tomato chr. 6 Roeland van Ham Centre for BioSystems Genomics The Netherlands.

SOL 2008 October 12-16, Cologne, Germany CHROMOSOME 7 THE FRENCH CONTRIBUTION TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497 T0676 TM18 CT54 T0966.

Tomato Overgo Project and Seed BAC Selection Cornell Team Ying Eileen Wang, 2005 PAG.

Mapping and sequencing chromosome 6 of Solanum lycopersicum cv

Solanum lycopersicum Chromosome 4 Sequencing Update UK-SOL– Dec 2008 Wellcome Trust Medical Photographic Library.

Current Sequencing Status of Tomato Chromosome 2 PLANT GENOME RESEARCH CENTER, KRIBB, KOREA Sanghyeob Lee Sung-Hwan Jo Dal-Hoe Koo Chul-Goo Hur Hong-Seok.

4th Solanaceae Genome Workshop 2007, September 09th- 13th, Jeju Island, Korea THE FRENCH CONTRIBUTION TO THE INTERNATIONAL TOMATO GENOME SEQUENCING PROGRAM.

FINISHING WORKSHOP APRIL 2008 CHROMOSOME 7 THE FRENCH CONTRIBUTION TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497 T0676 TM18 CT54 T0966 T0731 TM15.

15 January 2006, PAG XIV SanDiegoRémy Bruggmann, MIPS/IBI, GSF A Bioinformatic Framework to Unravel the Secrets of the Tomato Genome.

© 2010 by The Samuel Roberts Noble Foundation, Inc. 1 The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA 2 National Center.

Finishing tomato chromosomes #6 and #12 using a Next Generation whole genome shotgun approach Roeland van Ham, CBSG, NL René Klein Lankhorst, EUSOL Giovanni.

Chromosome 2 Doil Choi, Sunghwan Jo KOREA. Cytological architecture of chromosome kb/µm DAPI (4’-6-diamidino-2-phenylindole) stained pachytene chromosome.

Progress tomato chromosome 6 René Klein Lankhorst.

INDIAN INITIATIVE FOR TOMATO GENOME SEQUENCING Nagendra Singh National Research Centre on Plant Biotechnology Indian Agricultural Research Institute New.

中国农业科学院蔬菜花卉研究所 Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences Zhonghua Zhang Institute of Vegetables and Flowers, Chinese.

Comparative analyses of the potato and tomato transcriptomes

Chromosome 12 M. Pietrella 1, G. Falcone 1, E. Fantini 1, A. Fiore 1, C. Perla 1, M.R. Ercolano 2, A. Barone 2, M.L. Chiusano 2, S. Grandillo 3, N. D’Agostino.

Chromosome 12 M. Pietrella 1, G. Falcone 1, E. Fantini 1, A. Fiore 1, M.R. Ercolano 2, A. Barone 2, M.L. Chiusano 2, S. Grandillo 3, N. D’Agostino 2, A.

Wageningen, April 24-25, 2008 II Tomato Finishing Workshop Chromosome 12 Update ENEA, Rome University of Naples ‘Federico II’ CRIBI and Univ. of Padua.

HeterochromatinEuchromatin Relative chromosome length Relative bivalent diameter X 1.23 X 1.00 Relative area Relative optical density.

UK NGS Sequencing Update July 2009 Dr Gerard Bishop - Division of Biology Dr Sarah Butcher – Centre for Bioinformatics.

2nd TOMATO FINISHING WORKSHOP chromosome 9 Wageningen, April 24-25, 2008.

Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano Maria Luisa Chiusano Maria Raffaella Ercolano University.

The Genome Assemblies of Tasmanian Devil Zemin Ning The Wellcome Trust Sanger Institute.

Progress on sequencing tomato chromosome N22 (Chromosome 12—Telomere P) Stack Lab--April 8,2005 LE_HBa0045N22 LE_HBa0026C13 Estimated euchromatin.

Solanum lycopersicum Chromosome 4 Mapping and Finishing Update SRC-UK and Wellcome Trust Sanger Institute SOL Korea – September 2007 Wellcome Trust Medical.

Lindsay A. Shearer1, Lorinda K

The Wellcome Trust Sanger Institute

Day Two. DAY TWO 9:00 – 9:10Recap of day one 9:10 – 9:55TOPAAS demo (Sander) 9:55 – 10:15Coffee break 10:30 – 11:30New Technology Data 11:30 – 12:30High.

13 th January 2008 Plant & Animal Genome Conference Progress with Sequencing Tomato Chromosome 4 Clare Riddle Tomato Project Group Wellcome Trust Sanger.

16 th April 2007 Christine Nicholson, Mapping Core Group Wellcome Trust Sanger Institute Tomato Chromosome 4 Mapping & Use of FPC Copyright Wellcome Trust.

26 th July 2006 Christine Nicholson, Mapping Core Group Karen McLaren, Finishing Group Leader Wellcome Trust Sanger Institute Sequencing the Gene Space.

1 Comparative analyses of the potato and tomato transcriptomes David Francis, AllenVan Deynze, John Hamilton, Walter De Jong, David Douches, Sanwen Huang,

US Contribution to the International Tomato Genome Sequencing Effort Current structure of contributions Ongoing activity summary Funding issues.

CURRENT STATUS ON SEQUENCING OF CHROMOSOME 12 Mara Ercolano Ischia, 2005.

Tomato Sequencing Project Meeting at SOL 2008, Oct. 15, 2008

Plant & Animal Genome Conference

Development of genome sequencing infrastructure and progress toward sequencing of chromosomes 1, 10 and 11 Steve Tanksley, Cornell U Steve Stack, Colorado.

Sequencing Chromosome 2

Status of the US contribution to the international

Progress on sequencing tomato chromosome 12

Progress in sequencing chromosome 6

Current Sequencing Effort of Tomato Chromosome 2 - Chromosome assembly - Finishing workshop April KRIBB/SNU, Korea.

Progress in sequencing chromosome 6

TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497 T0676 TM18 CT54 T0966 T0731 TM15 T1347 T1257 T0848 THE FRENCH CONTRIBUTION TO THE INTERNATIONAL.

Sequencing update of tomato chromosome 3 Chinese Academy of Sciences

Tomato FISH Song-Bin Chang Suzanne Royer Lorrie Anderson Steve Stack.

SOL Jeju Island, Korea 14th September 2007

The Potato Genome Sequencing Consortium: An Update

Presentation transcript:

Solanum lycopersicum Chromosome 4 Sequencing Update SOL Germany– October 2008 Wellcome Trust Medical Photographic Library

Summary of Project Status at WTSI WTSI will be leaving the project on 31 st Oct 2008 Transfer of BAC selection/contig building QC- checking is on the move to Imperial College London Introduction

WTSI Tomato Clone Pipeline Pipeline Stage Number of BACs 2007 Number of BACs 2008 Subcloning340 Shotgun211 Assembly Start70 Auto-prefinishing30 Finishing1133 QC Checking42 Finished63147 Total Phase 3 Phase 1+2 HTGS:

Chromosome 4 Sequence Generated Total Sequence Available19,815,026 bp Total Unique Sequence19,527,597 bp Total amount of Finished Sequence = 15,244,914 bp

Some facts and figures We have 81 contigs on chr4 (80 contigs with sequence available). Average contig length is just under 250 kb. The average number of BACs per contig is 2.3. The largest sequence contigs are in the range of 450kb-500kb with 5 or 6 BACs.

Distribution of tomato Chromosome BACs and sequence content Centromere = Euchromatin = Heterochromatin 62 markers 41 markers 124 markers 30 contigs11 contigs 36 contigs 56 BACs 59 BACs63 BACs SSR markers 4 contigs 5 BACs UNORDERED 27 markers16 markers61 markers

Summary of Progress on Chromosome 4 81 map contigs have been built on chromosome 4 (AGP files) 119 BACs/44 contigs definitely on chr4 in FISH/ IL mapped 58 BACs under confirmation but have chr4 marker sequence ~60 Markers for which BACs have not been identified. ~13 BACs have been sequenced to HTGS3 and placed on chr0, definitely not on chr4 (others initiated, in same contig etc but stopped in pipeline). 22 Missing markers missing sequence?

Summary of what we will do next 1) Confirm chr4 location of BACs that lack chr4 marker sequence and or have conflicting map location. IL mapping. 2) Use missing marker sequences to identify further BACs (3D pools) and confirm chr4 location using IL mapping. 3) Use 3D BAC pools to identify BACs to extend current contigs. 4) Analyse output from X2 GS-FLX and X2 Illumina sequencing runs on cDNA from chr4 IL and parental lines to identify SNPs and further chr4 markers. 5) Use any markers from (4) to isolate further BACs for sequencing.

Acknowledgements Wellcome Trust Sanger Institute: Carol Churcher Jane Rogers Sean Humphray Clare Riddle and Mapping Core Group Karen McLaren and Finishing Team 46 Stuart McLaren and Pre-finishing Team 58 Christine Lloyd and QC Team 57 Karen Oliver Matt Jones Carol Scott Imperial College London: Gerard Bishop Daniel Buchan James Abbott Sarah Butcher Rosa Lopez-Cobollo University of Nottingham: Graham Seymour Scottish Crop Research Institute: Glenn Bryan Cornell University: Lukas Mueller Jim Giovannoni MIPS/IBI Institute for Bioinformatics: Klaus Mayer Remy Bruggmann FISH Resources Stephen Stack Group (Colorado) Hans de Jong (Wageningen) Dora Szinay (Wageningen) FUNDING